As an aside, this works for any media file, not just eBooks, and regardless of whether you chose to let iTunes manage your folders or not.
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tubedoggSep 3 '13 at 12:34

Thanks for the answers, but I was looking for a way to get the entire list in one shot, hoping that it's stored, say, in an XML file somewhere.
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wswSep 3 '13 at 14:19

Can you make another question to ask that? By the way, are you aware of the possibility of consolidating a library? (putting all the items in the same place... even if you initially didn't tell iTunes to organize it)
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ozkeSep 3 '13 at 14:26

ozke: I much prefer the way I manage eBooks on the Kindle -- I use Calibre to organize my book collection, and use rsync to sync the entire directory (recursively) to the device.
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wswSep 3 '13 at 21:05

Yeah, I'd also let people sort out their data the way they want. However, that's the way iTunes works I'm afraid. :S
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ozkeSep 4 '13 at 9:49